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- PDB-5hr3: Crystal structure of thioredoxin N106A mutant -

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Basic information

Entry
Database: PDB / ID: 5hr3
TitleCrystal structure of thioredoxin N106A mutant
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / thioredoxin / thiol redox-reactions
Function / homology
Function and homology information


DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / ETHANOL / Thioredoxin / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.101 Å
AuthorsNoguera, M.E. / Vazquez, D.S. / Howard, E.I. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
CitationJournal: Sci Rep / Year: 2017
Title: Structural variability of E. coli thioredoxin captured in the crystal structures of single-point mutants.
Authors: Noguera, M.E. / Vazquez, D.S. / Ferrer-Sueta, G. / Agudelo, W.A. / Howard, E. / Rasia, R.M. / Manta, B. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
History
DepositionJan 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9308
Polymers23,5512
Non-polymers3796
Water3,369187
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9494
Polymers11,7761
Non-polymers1733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9814
Polymers11,7761
Non-polymers2063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.238, 33.124, 47.185
Angle α, β, γ (deg.)75.750, 88.850, 68.830
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))
21(chain B and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLYSLYS(chain A and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))AA2 - 573 - 58
12ASNASNILEILE(chain A and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))AA59 - 7260 - 73
13GLYGLYLEULEU(chain A and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))AA74 - 10375 - 104
14ALAALAALAALA(chain A and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))AA105 - 108106 - 109
21ASPASPLYSLYS(chain B and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))BB2 - 573 - 58
22ASNASNILEILE(chain B and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))BB59 - 7260 - 73
23GLYGLYLEULEU(chain B and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))BB74 - 10375 - 104
24ALAALAALAALA(chain B and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))BB105 - 108106 - 109

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Components

#1: Protein Thioredoxin


Mass: 11775.557 Da / Num. of mol.: 2 / Mutation: N106A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA, BN17_37301, ECs4714 / Production host: Escherichia coli (E. coli) / References: UniProt: C3SKR2, UniProt: P0AA25*PLUS
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: The drop was a 1:1 mix of protein (10 mg/ml, in water) and reservoir solution (100 mM sodium acetate, 4 mM CuSO4, 25 % ethanol, pH 4.25)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9202 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.1→16.227 Å / Num. obs: 59930 / % possible obs: 93 % / Redundancy: 2 % / Biso Wilson estimate: 10.06 Å2 / Rmerge(I) obs: 0.036 / Χ2: 1.067 / Net I/σ(I): 14.8 / Num. measured all: 117251
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.1-1.141.90.24257571.08389.2
1.14-1.181.90.18658321.07591
1.18-1.2420.15859201.07591.9
1.24-1.320.13559921.0792.9
1.3-1.3920.10660161.0693
1.39-1.4920.08360761.07194.6
1.49-1.6420.06161311.04394.7
1.64-1.8820.04661611.04695.6
1.88-2.3720.0362121.08596.1
2.37-501.90.02258331.06590.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIXdev_2247refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KEB

1keb


Resolution: 1.101→16.227 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 15.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1634 3032 5.06 %Random selection
Rwork0.1419 56885 --
obs0.143 59917 92.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.86 Å2 / Biso mean: 17.0237 Å2 / Biso min: 6.35 Å2
Refinement stepCycle: final / Resolution: 1.101→16.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1626 0 26 187 1839
Biso mean--25.28 24.69 -
Num. residues----214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111687
X-RAY DIFFRACTIONf_angle_d1.2032293
X-RAY DIFFRACTIONf_chiral_restr0.09266
X-RAY DIFFRACTIONf_plane_restr0.008293
X-RAY DIFFRACTIONf_dihedral_angle_d14.822623
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1189X-RAY DIFFRACTION6.144TORSIONAL
12B1189X-RAY DIFFRACTION6.144TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.101-1.1180.20161300.1912271240182
1.118-1.13630.20311260.18492505263190
1.1363-1.15590.1891250.16442509263491
1.1559-1.17690.17871170.15912605272291
1.1769-1.19950.19451400.15082535267592
1.1995-1.2240.17931340.1482625275992
1.224-1.25060.17061350.14812519265492
1.2506-1.27970.17821350.14162594272992
1.2797-1.31170.19121330.14082615274893
1.3117-1.34710.16081330.12862605273893
1.3471-1.38680.17161340.13132596273093
1.3868-1.43150.14711530.12812636278995
1.4315-1.48260.15831490.12512630277994
1.4826-1.54190.15011130.12692650276394
1.5419-1.61210.14841480.12542636278495
1.6121-1.6970.15211470.13032659280696
1.697-1.80320.17541700.13522638280896
1.8032-1.94220.14531370.13532676281395
1.9422-2.13720.17581430.13332654279796
2.1372-2.44560.15641600.13182699285997
2.4456-3.07770.16191520.14812708286098
3.0777-16.22840.15671180.15682320243883

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